@bonemap you can use any video editor. If you have the multi channel audio you can use shutter encoder to add it to or replace the audio on an existing movie (must be exactly the same length). If you need to do it for an avi virtual dub will do it. You will generally need to start with a 6 channel wav file for 5.1.
You are right the multichannel audio capabilities on the movie player are lacking. You can play multi channel audio fine though and although you cannot route on the fly you can change the channel order in your audio setup on your computer. Alternatively most modern sound cards will let you do routing and some like RME will let you control the routing with osc or midi.
If you need to route multi channel audio inside and SDI signal it’s pretty common to use an SDI audio embedder. This lets you combine the outputs from an audio mixer with the output of a video system and have control over line delays and channel order.